6 From Supramolecular Chemistry to Constitutional Dynamic Chemistry Jean-Marie Lehn ISIS, Université Louis Pasteur, Strasbourg and Collège de France, Paris, France Supramolecular chemistry is actively exploring systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by selfassembly from their components, on the basis of the molecular information stored in the covalent framework of the components and read out at the supramolecular level through specific interactional algorithms, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation. Applications of this approach in biological systems as well as in materials science will be described. The merging of the features: - information and programmability, - dynamics and reversibility, - constitution and structural diversity, points towards the emergence of adaptive chemistry. References [1] Lehn, J.-M., Supramolecular Chemistry: Concepts and Perspectives, VCH Weinheim, [2] Lehn, J.-M., Dynamic combinatorial chemistry and virtual combinatorial libraries, Chem. Eur. J., 1999, 5, [3] Lehn, J.-M., Programmed chemical systems: Multiple subprograms and multiple processing/expression of molecular information, Chem. Eur. J., 2000, 6, [4] Lehn, J.-M., Toward complex matter: Supramolecular chemistry and self-organization, Proc. Natl. Acad. Sci. USA, 2002, 99, [5] Lehn, J.-M., Toward self-organization and complex matter, Science, 2002, 295, [6] Lehn, J.-M., Dynamers : Dynamic molecular and supramolecular polymers, Prog. Polym. Sci., 2005, 30, 814. [7] Lehn, J.-M., From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry, Chem. Soc. Rev., 2007, 36, 151. CHEMISTRY: SCIENCE AT THE FRONTIER 7

7 Jean-Pierre Sauvage Institut de Chimie, Laboratoire de Chimie Organo-Minérale, Université Louis Pasteur CNRS/UMR 7177, Strasbourg, France Catenanes, Rotaxanes and Molecular Machines The field of catenanes and rotaxanes [1] is particularly active, mostly in relation to the novel properties that these compounds may exhibit (electron transfer, controlled motions, mechanical properties, etc ). In addition, catenanes represent attractive synthetic challenges in molecular chemistry. The creation of such complex functional molecules as well as related compounds of the rotaxane family demonstrates that synthetic chemistry is now powerful enough to tackle problems whose complexity is sometimes reminiscent of biology, although the elaboration of molecular ensembles displaying properties as complex as biological assemblies is still a long-term challenge. The most efficient strategies for making such compounds are based on template effects. The first templated synthesis [2] relied on copper(i). The use of Cu(I) as template allows to entangle two organic fragments around the metal centre before incorporating them in the desired catenane backbone. Organic templates assembled via formation of aromatic acceptor-donor complexes or/and hydrogen bonds have also been very successful. Nowadays, numerous template strategies are available which have led to the preparation of a myriad of catenanes and rotaxanes incorporating various organic or inorganic fragments and displaying a multitude of chemical or physical functions. A particularly promising area is that of synthetic molecular machines and motors [3]. In recent years, several spectacular examples of molecular machines leading to real devices have been proposed, based either on interlocking systems or on non interlocking molecules [4]. In parallel, more and more sophisticated molecular machines have been reported, frequently based on multicomponent rotaxanes. Particularly noteworthy are the musclelike compounds reported by two groups [5,6], a molecular elevator [7], illustrating the complexity that dynamic threaded systems can reach. One of the prototypical systems is a bistable catenane whose motions are triggered by an electrochemical signal. The compound and its various forms are represented in Figure 1 [4a]. Copper is particularly well adapted to the design of molecular machines since its two oxidation states have distinct stereo-electronic requirements: whereas copper(i) is fully satisfied in a 4-coordinate (tetrahedral) geometry, copper(ii) requires more ligands in its coordination sphere. A5-coordinate situation is more adapted to the divalent state, as illustrated on Figure 1, Cu(II) being coordinated to both a 1,10-phenanthroline ligand and a 2,2,2,6 - terpyridine. Figure 1. The prototypical bistable copper-complexed catenane. The compound undergoes a complete metamorphosis by oxidising Cu(I) or reducing Cu(II). The process is quantitative but slow. In the course of the last 12 years, the response times of the various molecular machines made in Strasbourg have been considerably shortened. The fastest system is a rotaxane, able to undergo a pirouetting motion under the action of the same redox signal as for the catenane (Cu II /Cu I ) and whose axis incorporates a non sterically hindering chelate of the 2,2 -bipyridine type. Now, the motions take place on the micro- to milli-second timescale [8]. In recent years, our group has also proposed transition metal-based strategies for making twodimensional interlocking and threaded arrays [9]. Large cyclic assemblies containing several copper(i) centres could be prepared which open the gate to controlled dynamic two-dimensional systems and membrane-like structures consisting of multiple catenanes and rotaxanes. Two examples are presented in Figure th LILLY FOUNDATION SCIENTIFIC SYMPOSIUM

9 Fluorous Mixture Synthesis of Natural Product Stereoisomer Libraries Dennis P. Curran Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA Much current work in the field of fluorous chemistry relies on the use of fluorous stationary phases for separation. Following the introduction of fluorous tagging in 1996, [1] we soon introduced the technique of fluorous solid phase extraction (FSPE) [2]. The FSPE separation (Figure 1) allows the use of smaller (and therefore lighter) fluorous tags, and the method is especially useful for small scale discovery chemistry and library applications in drug discovery and other areas [3]. A recent review of FSPE features almost one hundred papers that have used the technique [4]. Scores of light fluorous reagents, reactants, catalysts, scavengers and protecting groups are now commercially available from Aldrich, Waco and Fluorous Technologies, Inc.[5] Our studies on FSPE soon led us to fluorous HPLC experiments, and this in turn led to the introduction of fluorous mixture synthesis,[6] a technique that we have since used in many new guises. The underlying concepts behind fluorous mixture synthesis, Figure 2, are those of solution phase mixture synthesis with separation and identification tagging. Briefly, a series of substrates is tagged with a homologous series of fluorous tags. The resulting tagged substrates are mixed and then taken through a multistep synthesis to provide a mixture of tagged products. During this mixture synthesis phase, effort is saved proportional to the number of compounds that are mixed. Finally, the last mixture is demixed by fluorous HPLC to provide the individual tagged products, which are then detagged (deprotected) to provide the final target compounds The concepts of solution phase mixture synthesis are general, and Craig Wilcox introduced a new class of oligoethylene (OEG) tags[7]. Figure 1. Fluorous Solid Phase Extraction: Separates tagged compounds (orange fraction) from untagged ones (blue fraction) by a generic filtration-like process. Figure 2. Concepts of Fluorous Mixture Synthesis: Substrates are tagged and mixed. Mixture synthesis then precedes demixing and detagging. Soon after the introduction fluorous quasiracemic synthesis [8], we introduced the concept of complete stereoisomer libraries [9] (made by fluorous mixture synthesis), a concept that has been featured in much of our natural products work since then. We later united fluorous and OEG tags in the technique of double mixture synthesis [10]. These techniques have gone well beyond proof-of-principle ; the derived products (see Figure 3) have been used to solve structure problems and provide importance biological information[11,12] th LILLY FOUNDATION SCIENTIFIC SYMPOSIUM

11 Alois Fürstner Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany The Awesome Power of Metathesis Although olefin metathesis had already been discovered during early studies on Ziegler polymerization and had found industrial applications shortly thereafter, it was not until the 1990 th that this transformation gained real significance for advanced organic synthesis. The last decade, however, has seen an explosive growth of interest in metathetic conversions in general, making clear that this reaction is one of the most fascinating and versatile processes in the realm of homogeneous catalysis. Scheme 1. Basic catalytic cycle of RCM. Alkene metathesis refers to the redistribution of the alkylidene moieties of a pair of olefins effected by catalysts that are able to cleave and to form C-Cdouble bonds under the chosen reaction conditions. This mutual alkylidene exchange occurs via a sequence of formal [2+2] ycloadditions/cycloreversions (Chauvin mechanism)[1] involving metal alkylidene and metallacyclobutane species as the catalytically competent intermediates. Among the many possible uses of metathesis, the ring closing olefin metathesis (RCM) of dienes to cycloalkenes depicted in Scheme 1 remains particularly popular. It was the development of well defined metal alkylidene complexes combining high catalytic activity with an excellent tolerance towards polar functional groups that has triggered this avalanche of interest. The most prominent and versatile ones are molybdenum alkylidenes developed by Schrock[2] and five coordinate ruthenium carbene complexes introduced by Grubbs (Scheme 1)[3]. These commercially available complexes define the standard in the field and have reached an immense popularity as witnessed by a truly prolific number of successful applications. They also serve as lead structures for the development of even more powerful second generation catalysts bearing N- heterocyclic carbenes as ancillary ligands. The latter effect even the formation of tetrasubstituted cycloalkenes and are sufficiently reactive to activate electron deficient? as well as certain electron rich alkenes that were beyond reach of the parent Grubbs catalyst. RCM is essentially driven by entropy; the ensuing equilibrium is constantly shifted towards the cycloalkene by loss of ethylene (or another volatile olefin) formed as the by-product (cf. Scheme 1). The inherent competition between cyclization of a given diene and its polymerization via acyclic diene metathesis (ADMET) strongly depends on the ring size formed as well as on pre-existing conformational constraints and can be influenced to some extent by adjusting the dilution. While five to sevenmembered carbo- and heterocycles usually form without incident, medium- and large rings are more delicate and deserve careful consideration during retrosynthetic planning. It is known that chelation of the metal carbene intermediates by the polar substitutents in the substrates plays a decisive role for productive macrocyclization [4]; hence, proper analysis of the donor strength of the heteroatoms, their distance and relative orientation towards the alkene groups allows for reliable planning even of complex target molecules of virtually any ring size. A few recent examples of bioactive compounds formed by RCM-based total synthesis protocols by our group are shown in Scheme 2 [5]. A major advantage of RCM over more conventional approaches stems from the exceptional chemoselectivity of the available metathesis 12 13th LILLY FOUNDATION SCIENTIFIC SYMPOSIUM

12 catalysts for the activation of olefins in the presence of most other functional groups. This, in turn, allows to avoid lengthy protecting group manipulations, thus rendering many metathesis based approaches unprecedentedly short and economic in the overall number of steps. As a consequence modern metathesis chemistry has a profound impact on the logic of synthesis. Its enormous relevance is further increased by the fact that the modern catalysts are fully operative under aqueous conditions as well as in unconventional media such as ionic liquids or supercritical CO 2. Despite this highly attractive overall profile and the maturity reached in recent years, several problems remain yet to be solved. One of the major challenges is the missing control over the geometry of the emerging double bond during RCM-based formations of macrocycles as well as in many cross metathesis reactions. One way to tackle this problem takes recourse to ring closing alkyne metathesis (RCAM) followed by semi-reduction of the cycloalkynes thus formed (Scheme 3) [6]. This approach has been successfully implemented into various total syntheses, including a fully selective and high yielding route to the promising anti-cancer agent epothilone A [7]. Scheme 3. Ring Closing Alkyne Metathesis RCAM)/Semi- Reduction Selected Examples of Natural Products prepared by this Methodology References [1] Y. Chauvin, Angew. Chem. Int. Ed. 2006, 45, 3740 (Nobel lecture). [2] R. R. Schrock, Angew. Chem. Int. Ed. 2006, 45, 3748 (Nobel lecture). [3] R. H. Grubbs, Angew. Chem. Int. Ed. 2006, 45, 3760 (Nobel lecture). [4] a) A. Fürstner, K. Langemann, J. Org. Chem. 1996, 61, 3942; b) A. Fürstner, O. R. Thiel, C. W. Lehmann, Organometallics 2002, 21, 331. [5] A. Fürstner, Angew. Chem. Int. Ed. 2000, 39, [6] A. Fürstner, G. Seidel, Angew. Chem. Int. Ed. Engl. 1998, 37, [7] A. Fürstner, P. W. Davies, Chem. Commun. 2005, Scheme 2. Natural products prepared by our group via RCM. CHEMISTRY: SCIENCE AT THE FRONTIER 13

16 Domino and Multiple Pd-Catalyzed Reactions for the Efficient synthesis of Natural Products and Materials The development of efficient syntheses of bioactive compounds such as natural products and analogues, drugs, diagnostics, agrochemicals in academia and industry is a very important issue of modern chemistry [1]. In this respect, complex multistep syntheses have to be avoided since they are neither economically nor ecologically justifiable. Modern syntheses must deal carefully with our resources and our time, must reduce the amount of waste formed, should use catalytic transformations and finally must avoid all toxic reagents and solvents. In addition, synthetic methodology must be designed in a way that it allows access to diversified substance libraries in an automatized way. A general way to improve synthetic efficiency and in addition also to give access to a multitude of diversified molecules is the development of domino reactions which allow the formation of complex compounds starting from simple substrates in a single transformation consisting of several steps [1]. We have defined domino reactions as processes of two or more bond forming reactions under identical conditions, in which the subsequent transformations take place at the functionalities obtained in the former transformations. The quality and importance of a domino reaction can be correlated to the number of bonds generated in such a process and the increase of complexity, for which we have created the expression "bond forming efficiency". Domino reactions can be performed as single-, twoand multicomponent transformations. Thus, most of the known multicomponent processes [2] can be defined as a subgroup of domino reactions. Domino reactions can be classified according to the mechanism of the single steps which may be of the same or of different kind. As mechanistical differentiation we have included cationic, anionic, radical, pericyclic, transition metal-catalyzed and redox transformations. A combination of mechanistically different reactions is the domino-knoevenagel-hetero-diels-alder reaction, which was developed in my group and which has emerged as a powerful process which not only allows the efficient synthesis of complex compounds such as natural products starting from simple substrates but also permits the preparation of highly diversified molecules. Lutz F. Tietze Institute of Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany It consists of a Knoevenagel condensation [3] of generally an aldehyde with a 1,3-dicarbonyl compound in the presence of catalytic amounts of a weak base such as ethylene diammonium diacetate (EDDA) or piperidinium acetate. In the reaction a 1- oxa-1,3-butadiene is formed as intermediate which can undergo a hetero-diels-alder reaction [4] either with an enol ether or an alkene. The procedure has been used by us among others for the synthesis of several alkaloids (Scheme 1). Scheme 1. Enantiopure alkaloids synthesized by a three or four component domino-knoevenagel-hetero-diels-alder reaction Another highly fruitful approach consisting of a Pdcatalyzed nucleophilic substitution of an allyl acetate followed by a Pd-catalyzed arylation of an alkene was used in the synthesis of ( )-cephalotaxine. The starting material for this process was obtained via an enantioselective CBS-reduction of the corresponding 2 bromocyclopentenone; moreover, the reaction proceeds with high diastereoselectivity forming only one diastereomer. Scheme 2. Synthesis of ( )-cephalotaxine CHEMISTRY: SCIENCE AT THE FRONTIER 17

18 DNA Charge Transport Chemistry and Biology Jacqueline K. Barton Division of Chemistry and Chemical Engineering. California Institute of Technology. Pasadena, CA, USA Our laboratory has been interested in exploring both the fundamentals of how electrons and holes migrate through the base pair stack as well as the biological implications of this chemistry with respect to how DNA may be damaged and repaired. From our laboratory and others it has by now been demonstrated in a range of different experiments that double helical DNA does indeed mediate the efficient transport of charge, both electrons and holes, on timescales as short as picoseconds. [1] Moreover, recently our laboratory has focused studies on determining how the cell may harnass this chemistry to facilitate redox signaling among proteins bound to DNA, to funnel damage to specific sites and activate repair of damage to DNA. [2] The ability of DNA to serve as a medium for the transport of charge is intrinsic to its p-stacked structure. The B-DNA double helix is an array of heterocyclic aromatic base pairs, stacked at a distance of 3.4 Å, wrapped within a negatively charged sugar phosphate backbone. (Figure 1) This analogy between DNA and solid state p-systems is useful in considering DNA charge transport: the interactions between the p-electrons of the DNA base pairs provide the electronic coupling necessary for DNA charge transport to occur. But it is important to consider also the differences between DNA, a p- stacked macromolecular assembly in solution, and solid state p-stacks. In contrast to solid state p-stacks, DNA is conformationally dynamic, a property that is key to all of its biological functions. Conformational rearrangements of the DNA bases on the ps to ms time scale modulate base stacking interactions, redox potentials, and electronic coupling between the DNA bases. Thus the sequence-dependent dynamical motions of DNA both facilitate and inhibit long range charge transport through the base pair stack. [4] Charge transport through the base pair stack is gated by the motions of the DNA bases. Using electrochemical, biochemical, and biophysical measurements, we have now characterized some of the important features of DNA charge transport chemistry. [5] Importantly, we have found that charge transport through DNA can occur over very large molecular distances, > 200 Å. [6,7] In DNA assemblies containing a pendant photooxidant, we have shown that hole transport through the DNA duplex can promote oxidative damage to guanine doublets far from the site of the pendant oxidant. (Figure 2) Moreover this chemistry is independent of the oxidant utilized. It is a property of the DNA base pair stack. Figure 1. An illustration of the stacked base pairs in DNA looking across the helix (above) and down the helix axis (below). It is no surprise that shortly after the double helical structure was proposed by Watson and Crick, scientists asked whether inherent in the structure of stacked base pairs there might be another functional property of DNA. Given the similarity to one dimensional aromatic crystals, it was proposed that the DNA p-stack might be a conduit for rapid and efficient charge migration. [3] Figure 2. As schematically illustrated, in a DNA assembly with tethered photooxidant (red), oxidative damage to guanine doublets (yellow) can be promoted over long distances through DNA charge transport. This property is interesting to consider in the context of reactions within the cell. Indeed, we have also shown that DNA hole transport can proceed in the nucleosome core particle to effect damage to DNA from a distance. [8] Hence while DNA may be CHEMISTRY: SCIENCE AT THE FRONTIER 19

19 packaged into chromatin, protecting the DNA library from the onslaught of harmful agents, this chromatin structure cannot protect the DNA from long range oxidative damage through DNA charge transport. Perhaps instead Nature funnels damage to particular sites, protecting others. [2] It is interesting also to note that we have demonstrated not only damage to DNA promoted from a distance but also the oxidation of DNA-bound proteins from a distance. [9] In particular, p53, a critically important cell cycle regulatory protein, bound to some promoters but not others can be oxidized from a distance leading to its dissociation from the DNA. We have proposed that this long range chemistry may provide a global signaling of oxidative stress within the cell, yielding the dissociation of p53 from some promoters but not others so as to activate the cell to respond to the conditions of oxidative stress. While DNA charge transport can proceed over long molecular distances, another critical characteristic of this chemistry is the exquisite sensitivity to perturbations in the intervening base stack. Single base pair mismatches, base lesions, and the structural changes associated with protein binding all lead to an inhibition of DNA charge transport. [5] (Figure 3) Figure 4. DNA-mediated electrochemistry to a redox probe (blue). This electrochemistry is, however, inhibited by an intervening mismatch (red). found, excise the damage, repairing the genome. Interestingly, biquitous to a subset of these base excision repair enzymes are 4Fe-4S clusters, a common redox cofactor in biology. Although these clusters are not redox-active in the absence of DNA, we have demonstrated using DNA-modified electrodes that, in the presence of DNA, their potentials are shifted to a physiologically relevant range. [12,15] DNA binding thus facilitates oxidation of the clusters in a DNAmediated reaction. We have furthermore demonstrated that this potential shift is general to a range of DNA repair proteins that contain the 4Fe-4S clusters, and we have proposed DNA-mediated signaling among different repair Figure 3. Illustrations of perturbations that inhibit long range charge transport through DNA: (left) DNA bulges; (center) DNA mismatches; (right) protein binding that kinks the DNA. We have demonstrated this sensitivity in not only through experiments monitoring an attenuation in long range oxidative damage but also in DNA electrochemistry experiments that monitor the attenuation in redox signal as a function of intervening perturbations in the base pair stack. [10,11] (Figure 4) This sensitivity in DNA charge transport to p-stacking perturbations has led to the development of novel biosensors capable of the detection of single base mismatches, lesions and DNA-protein interactions. Given this remarkable sensitivity of DNA charge transport in detecting DNA lesions, we have also asked whether Nature may harnass this chemistry also in the first steps of DNA repair, where base lesions are first detected. [12,14] Within cells there is an extraordinary repair machinery, the base excision repair enzymes, which constantly monitor the genome for base damage, and once proteins bound to DNA in detecting base lesions. Essentially analogous to telephone repairmen looking for a break in the telephone line, proteins can carry out DNAmediated electron transfer reactions with one another as long as the intervening DNA is intact; these electron transfers facilitate protein dissociation and a search of the genome. However, if there is an intervening lesion, DNA-mediated charge transport is inhibited, the proteins do not dissociate, and instead remain in the vicinity to repair the lesion. Hence this chemistry provides a means to redistribute the repair proteins where they are needed in the vicinity of the DNA lesion. We are now focused on delineating how DNA charge chemistry plays a role in the activity of base excision repair proteins as well as asking whether other DNAbinding proteins that contain redox cofactors may similarly employ DNA-mediated charge transport for long range signaling. Certainly this chemistry is unique in that the chemistry can occur with control over long molecular distances but with a remarkable sensitivity to intervening perturbations. There is 20 13th LILLY FOUNDATION SCIENTIFIC SYMPOSIUM

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